README.md

# DataModelingGeneExpressions
## Setup
Clone this repository into the directory of your choosing. Ensure that you have php and the necessary depencies installed. Once done, ensure the necessary mySQL username and password information in the following files:

> 1. src/connection.php
> 2. scripts/addGSE.py
> 3. scripts/cohortPairQuerier.py
> 4. scripts/cohortQuery.py
> 5. scripts/populationQuery.py
> 6. scripts/Querier.py
> 7. scripts/setup.py
> 8. scripts/truncate.py

Once the correct information is filled your, create a database with the name `dataModelingGeneExpressions`. Then, in the `src` directory, run the `setup.py` script. This will create the necessary tables, and populate the Concept Hierarchy Tree used in the querying scripts. 


## Using Application
Once setup, begin the application. From here, click `register`, enter information to your desires, and login. Utilize the `add GSE` page to populate database.

## Quickly Populate Database
Navigate to `scripts/addGSE.py`. You will find the following code at the bottom:

```python
if __name__ == '__main__':
    import sys
    arg = sys.argv[1]
    main(arg)
    # for i in range(70093, 70100):
    #     gse = "GSE" + str(i)
    #     main(gse)
```

Comment the first three lines within the if statement, and uncomment the last thre lines like so:
```python
if __name__ == '__main__':
    # import sys
    # arg = sys.argv[1]
    # main(arg)
    for i in range(70093, 70100):
        gse = "GSE" + str(i)
        main(gse)
```
Change the range values as needed, and run the script. 
**Be sure to revert the changes once done.**